The aim of the paper is to demonstrate the application of system identification technique to estimate the hydrodynamic derivatives with the full-scale manoeuvring data of a ship. The application of such technique would be for design of autopilots, enhancement of manoeuvring characteristics of ships in service and validation of mathematical model for ship manoeuvring. The paper briefly describes the mathematical model for ship manoeuvring used for parameter identification of a bulk carrier using extended Kalman filter system identification technique. The standard manoeuvres conducted in line with the recommendations of International Maritime Organization (IMO) resolution 137 include turning circle trials and crash stop trial details are presented and using extended Kalman filter technique hydrodynamic derivatives are estimated. This paper includes also the full scale trial data of a inshore patrol vessel. © Springer Nature Singapore Pte Ltd. 2019.